AMBER Archive (2009)

Subject: Re: [AMBER] prot-DNA simulation

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Wed Jan 21 2009 - 15:55:52 CST

> I want to put a protein-RNA structure on dynamics. I was confused as to
> which force field is best suited for the purpose?

The nucleic acid force fields in AMBER are: ff94, ff98, ff99, and ff99+parmbsc0

The (non-polarizable) all-atom protein force fields are: ff94, ff96, ff99,
ff99SB, ff03

The best overlap is likely the ff99+parmbsc0 and ff99SB (i.e. ff99SB plus
the parmbsc0 modifications/frcmod) since these use a similar charge
derivation philosophy and a number of high quality simulations of proteins
and/or RNA have resulted with this combination.

Avoid ff94, ff96, ff99 for proteins as mentioned on the reflector
previously as these have a misbalance between alpha and beta conformations
(among other deficiencies).

For DNA I would recommend ff99+parmbsc0; this combination corrects a
deficiency most notable in (long) DNA duplex simulations where a funny
substate becomes dominate, specifically alpha/gamma = g+, t. This
transition occurs in RNA too but is less dominant. The parmbsc0 gets rid
of this however the bias of gamma away from trans maybe too high. Towards
this end, if you are simulating an RNA-protein complex, look at your RNA
structure and see if the experimental structure has gamma=trans anywhere.
If it does, then it is a research question as to which force field is
better.

If doing DNA, definately use parmbsc0, as ff99 is wrong; and also note
whether the experimental structure has any gamma=trans. If it does
parmbsc0 will move towards more canonical values. If there are lots of
gamma=trans in the starting structure, ff99 may be appropriate, but note
that if you run for more than ~5-10ns, other gamma=trans substates will
become populated.

Clear as mud?

--tom

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham

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